LPS-MIA base analysis

Post-normalization QC

  1. Performing post-normalization QC:

Post-correction QC

  1. Post-correction QC

Something that might make you sad: this is how the data looks when we can remove duplicate correlation:

DESeq2 anaylsis

  1. Performing DESeq2

out of 17645 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 0, 0% LFC < 0 (down) : 0, 0% outliers [1] : 0, 0% low counts [2] : 0, 0% (mean count < 1) [1] see ‘cooksCutoff’ argument of ?results [2] see ‘independentFiltering’ argument of ?results

Interactive results table

(5.1) Results

Patir et al. microglia markers

  1. Composite microglia marker score:
                    PC1        PC2         PC3        PC4         PC5

OH1-5B4D38CTR1 -1.74636258 2.8908017 1.02848364 2.5834555 -2.19440657 OH1-5B4D38CTR2 -1.00208645 0.6358254 -0.01398362 -0.4047980 2.03101594 OH1-5B4D38CTR3 -3.41508531 2.2693310 1.99621374 -1.1706207 -0.43971717 OH1-5B4D38LPS1 3.19382859 -2.1848698 -0.22014013 -0.5797534 0.88232874 OH1-5B4D38LPS2 0.54966486 -1.9875982 -4.72708866 1.6562309 -0.38398223 OH1-5B4D38LPS3 2.42004089 -1.6234901 1.93651503 -2.0845143 0.10476129 OH1-5B5D38CTR_1 -2.62972927 0.5794867 1.14752562 0.5710132 0.09500758 OH1-5B5D38CTR_2 0.75762124 1.3138442 -2.50090371 0.9778932 0.41035087 OH1-5B5D38CTR_3 1.67752849 1.3791259 0.29815748 -1.4062183 2.09530128 OH1-5B5D38LPS_1 2.07546124 -0.4512134 -0.12650997 1.0443274 0.12716672 OH1-5B5D38LPS_2 -0.53319395 -0.9457336 0.03402299 -1.6296096 -0.70720060 OH1-5B5D38LPS_3 -1.34768775 -1.8755098 1.14770758 0.4425942 -2.02062584 OH2-6B5D38CTR_1 10.17233506 2.0764612 0.41221900 -0.1750392 -0.92630455 OH2-6B5D38CTR_2 -4.01474252 1.2175377 -1.18427120 -1.0939976 1.02699449 OH2-6B5D38CTR_3 -3.19550551 1.3053340 -2.41939479 -1.4331930 -0.27125948 OH2-6B5D38LPS_1 0.04033274 -0.3485140 0.63748910 0.5721122 -0.94188988 OH2-6B5D38LPS_2 -2.45517285 -2.0958791 0.73582794 0.2377475 0.47652628 OH2-6B5D38LPS_3 -0.54724693 -2.1549398 1.81812994 1.8923702 0.63593315 PRO1B2CTR1D37 0.32692134 0.3375157 -0.67431100 -0.6502875 -0.77925089 PRO1B2CTR2D37 0.40579229 1.0141065 0.62233632 0.9588242 1.06056554 PRO1B2CTR3D37 0.61552080 1.1320469 -0.98752565 -1.0191720 -0.69814332 PRO1B2LPSD37_1 0.10321043 0.1890856 1.05778546 2.6107954 2.04463051 PRO1B2LPSD37_2 -0.71134949 -1.2447647 0.13640154 -1.6037324 -0.90367939 PRO1B2LPSD37_3 -0.74009537 -1.4279899 -0.15468666 -0.2964278 -0.72412245 PC6 PC7 PC8 OH1-5B4D38CTR1 0.21480100 -1.91113616 1.1044137 OH1-5B4D38CTR2 1.98553343 1.06121083 1.0745311 OH1-5B4D38CTR3 -0.25665357 2.36892821 -1.4395639 OH1-5B4D38LPS1 -2.02010049 -1.49275215 0.2772924 OH1-5B4D38LPS2 -0.02764314 0.48593103 -0.8854534 OH1-5B4D38LPS3 0.10406277 -0.51218176 -0.1312199 OH1-5B5D38CTR_1 -0.42263670 -0.08905834 -0.5954873 OH1-5B5D38CTR_2 0.94704612 0.50107298 0.4288915 OH1-5B5D38CTR_3 1.34975022 -2.15171211 -0.9893739 OH1-5B5D38LPS_1 0.53255664 0.77311571 0.1877774 OH1-5B5D38LPS_2 -1.99598448 1.42034357 2.2008616 OH1-5B5D38LPS_3 -0.41073179 -0.45376181 -1.2326692 OH2-6B5D38CTR_1 -0.22919664 1.10087039 -0.3718179 OH2-6B5D38CTR_2 -1.46489700 -0.64857151 -0.8236197 OH2-6B5D38CTR_3 -0.85455874 -0.43438780 0.2496625 OH2-6B5D38LPS_1 0.50967516 -0.19661800 0.8486596 OH2-6B5D38LPS_2 1.59006809 0.75444472 1.1424221 OH2-6B5D38LPS_3 0.44890913 -0.57573780 -1.0453066 PRO1B2CTR1D37 1.42461907 -0.23824278 0.5731002 PRO1B2CTR2D37 -1.23915952 -0.12769537 0.6874805 PRO1B2CTR3D37 -0.01835041 -0.54801741 -0.9117108 PRO1B2LPSD37_1 -1.61494444 0.72936799 0.2050794 PRO1B2LPSD37_2 0.77958128 -0.83222264 1.2139144 PRO1B2LPSD37_3 0.66825402 1.01681021 -1.7678636

(7.1) Look at the PCA:

LPS response genes

  1. Composite LPS response score:
                    PC1           PC2           PC3          PC4

OH1-5B4D38CTR1 1.55468250 -8.509066e-01 0.2200962835 0.644432419 OH1-5B4D38CTR2 0.74812227 7.748052e-01 0.2731713915 -0.388676504 OH1-5B4D38CTR3 1.64861884 2.307332e-01 -0.4379126279 0.077374434 OH1-5B4D38LPS1 -2.05432042 -5.194201e-01 0.0493785410 0.530878039 OH1-5B4D38LPS2 -2.00689777 -7.866440e-02 -0.4864094472 -0.716735003 OH1-5B4D38LPS3 0.10979458 4.434526e-01 0.3816758592 -0.147273384 OH1-5B5D38CTR_1 0.36203233 1.658608e-01 -0.4407139455 -0.099854301 OH1-5B5D38CTR_2 0.34246086 -6.347020e-01 -0.1715099740 0.005502484 OH1-5B5D38CTR_3 0.68271969 -4.371753e-01 0.9409558116 -0.430837597 OH1-5B5D38LPS_1 -0.73884468 3.413154e-02 0.3551640008 -0.082803648 OH1-5B5D38LPS_2 -0.73721914 6.912883e-01 -0.2504483797 0.095995761 OH1-5B5D38LPS_3 0.08885094 1.805967e-01 -0.4334475131 0.511997301 OH2-6B5D38CTR_1 -0.19871539 -4.323615e-01 1.0919632696 -0.137609629 OH2-6B5D38CTR_2 0.23770593 -4.683400e-01 -1.0401435226 0.059818441 OH2-6B5D38CTR_3 0.80368881 7.173346e-02 -0.4240476855 -0.783784105 OH2-6B5D38LPS_1 -0.51985909 6.578935e-01 0.5110810152 0.286818295 OH2-6B5D38LPS_2 -0.03137982 9.208090e-01 -0.2884259429 0.327056587 OH2-6B5D38LPS_3 -0.29144044 -7.497344e-01 0.1495728663 0.247700411 PRO1B2CTR1D37 0.02209927 5.255697e-01 0.5177850650 -0.269422233 PRO1B2CTR2D37 -0.21320435 -4.745589e-01 0.0002228491 0.001116586 PRO1B2CTR3D37 -0.03461903 -2.029023e-05 0.1518442785 0.686809971 PRO1B2LPSD37_1 0.07053913 -1.197639e+00 -0.3109711644 -0.504500690 PRO1B2LPSD37_2 0.23895682 7.799898e-01 0.1299434992 0.046036331 PRO1B2LPSD37_3 -0.08377184 3.666590e-01 -0.4888245274 0.039960035 PC5 PC6 PC7 PC8 OH1-5B4D38CTR1 0.06530352 0.589759011 -0.096116485 0.318414999 OH1-5B4D38CTR2 -0.34020462 -0.239409304 0.204750455 -0.219434232 OH1-5B4D38CTR3 0.23193953 -0.369539165 0.077466053 -0.369406890 OH1-5B4D38LPS1 0.07956146 -0.026517595 0.131620459 -0.078818005 OH1-5B4D38LPS2 -0.07548374 0.019550748 -0.330250024 0.189284851 OH1-5B4D38LPS3 0.03888386 0.026156305 0.012529542 0.159959277 OH1-5B5D38CTR_1 -0.26271326 -0.004211853 -0.359999938 0.209426238 OH1-5B5D38CTR_2 0.04058866 0.333723075 -0.006759743 -0.152903934 OH1-5B5D38CTR_3 -0.37911028 -0.197952352 -0.044080806 0.117434410 OH1-5B5D38LPS_1 0.17363790 0.084809491 0.232148431 -0.200006629 OH1-5B5D38LPS_2 0.44379713 -0.024740063 0.203899828 -0.018017546 OH1-5B5D38LPS_3 -0.01620016 -0.191628298 -0.025207772 0.044067460 OH2-6B5D38CTR_1 0.47491100 0.047839174 -0.393969929 -0.363118366 OH2-6B5D38CTR_2 0.51752801 0.033429169 -0.111469115 -0.142540604 OH2-6B5D38CTR_3 0.07118162 -0.110000696 -0.134063150 0.275588745 OH2-6B5D38LPS_1 -0.54446154 0.332350731 0.048679161 0.001208301 OH2-6B5D38LPS_2 -0.39688074 0.217088703 0.111195712 -0.079313477 OH2-6B5D38LPS_3 -0.12227836 -0.520707080 0.479627320 0.308175401 PRO1B2CTR1D37 0.50045590 0.170479557 -0.097363788 -0.014719874 PRO1B2CTR2D37 0.01822542 -0.131622565 -0.138240993 0.199186210 PRO1B2CTR3D37 -0.21257723 -0.593986294 -0.476261588 -0.073491228 PRO1B2LPSD37_1 -0.37391206 0.147361642 0.483277987 -0.269211806 PRO1B2LPSD37_2 0.54464456 0.081617562 0.394699435 0.342763697 PRO1B2LPSD37_3 -0.47683659 0.326150098 -0.166111052 -0.184526999